3D Gene Expression

Expression Atlases
Search PointClouds
Browse PointClouds
Data Releases

Overview:
   Summary
   Project Goals

Methods:
   Staining & Mounting
   Probe Constructs
   Staging
   Imaging

Software:
   PointCloudXplore
   PointCloudToolBox
   PointCloudAlign
   NODE

File Formats:
   PointCloud (.pce)
   VirtualEmbryo (.vpc)
   Correspondence files

Software
The BDTNP is providing software developed to process, visualize and analyze 3D gene expression data.
  • PointCloudXplore: Visualization and analysis of the data in PointCloud and Virtual Embryo Files.
  • PointCloudToolBox: Image analysis methods to generate PointCloud files that contain geometric data for each nucleus (position, volume, etc.), and the measured levels of gene expression in a single embryo.
  • PointCloudAlign: Registration methods to place gene expression data from many embryos into a VirtualEmbryo file, to allow comparison between the expression patterns of more than two or three genes.
  • Nonparametric Identification of Regulatory Interactions (NODE): A method that determines the correlation between transcription factor protein concentrations and temporal changes in the mRNA expression of putative target genes for small clusters of cells throughout the embryo.
  • Biological Imaging Database (BID): A relational database, and web-based user interface, for tracking 3D gene expression experiments. The source code and instructions are available upon request.